text: # Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack.package import *
  
  
  class Grnboost(Package):
      """GRNBoost is a library built on top of Apache Spark that implements a
      scalable strategy for gene regulatory network (GRN) inference.
  
      See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md
      for the user guide. The location of xgboost4j-<version>.jar and
      GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to
      xgboost4j-<version>.jar is also added to CLASSPATH."""
  
      homepage = "https://github.com/aertslab/GRNBoost"
  
      version('2017-10-9', git='https://github.com/aertslab/GRNBoost.git',
              commit='26c836b3dcbb85852d3c6f4b8340e8655434da02')
  
      depends_on('sbt', type='build')
      depends_on('java', type=('build', 'run'))
      depends_on('xgboost', type='run')
      depends_on('spark+hadoop', type='run')
  
      def setup_run_environment(self, env):
          grnboost_jar = join_path(self.prefix, 'target',
                                   'scala-2.11', 'GRNBoost.jar')
          xgboost_version = self.spec['xgboost'].version.string
          xgboost_jar = join_path(self.spec['xgboost'].prefix,
                                  'xgboost4j-' + xgboost_version + '.jar')
          env.set('GRNBOOST_JAR', grnboost_jar)
          env.set('JAVA_HOME', self.spec['java'].prefix)
          env.set('CLASSPATH', xgboost_jar)
          env.set('XGBOOST_JAR', xgboost_jar)
  
      def install(self, spec, prefix):
          sbt = which('sbt')
          sbt('assembly')
          install_tree('target', prefix.target)
  